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Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials 期刊论文
COMMUNICATIONS BIOLOGY, 2024, 卷号: 7, 期号: 1, 页码: 13
作者:  Gong, Tiansu;  Ju, Fusong;  Bu, Dongbo
收藏  |  浏览/下载:11/0  |  提交时间:2024/05/20
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2023, 卷号: 20, 期号: 6, 页码: 3482-3488
作者:  Gong, Tiansu;  Ju, Fusong;  Sun, Shiwei;  Bu, Dongbo
收藏  |  浏览/下载:34/0  |  提交时间:2024/05/20
Deep learning  protein structure prediction  
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms 期刊论文
GENOMICS PROTEOMICS & BIOINFORMATICS, 2023, 卷号: 21, 期号: 5, 页码: 913-925
作者:  Huang, Bin;  Kong, Lupeng;  Wang, Chao;  Ju, Fusong;  Zhang, Qi;  Zhu, Jianwei;  Gong, Tiansu;  Zhang, Haicang;  Yu, Chungong;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:10/0  |  提交时间:2024/05/20
Protein folding  Protein structure prediction  Deep learning  Transformer  Language model  
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction 期刊论文
BIOINFORMATICS, 2022, 卷号: 38, 期号: 4, 页码: 990-996
作者:  Ju, Fusong;  Zhu, Jianwei;  Zhang, Qi;  Wei, Guozheng;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:27/0  |  提交时间:2022/12/07
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs 期刊论文
JOURNAL OF COMPUTATIONAL BIOLOGY, 2022, 页码: 14
作者:  Kong, Lupeng;  Ju, Fusong;  Zheng, Wei-mou;  Zhu, Jianwei;  Sun, Shiwei;  Xu, Jinbo;  Bu, Dongbo
收藏  |  浏览/下载:26/0  |  提交时间:2022/12/07
deep learning and protein threading  protein alignment  protein structure prediction  
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph 期刊论文
BMC Bioinformatics, 2021, 卷号: 22, 期号: 1
作者:  Huang,Bin;  Wei,Guozheng;  Wang,Bing;  Ju,Fusong;  Zhong,Yi;  Shi,Zhuozheng;  Sun,Shiwei;  Bu,Dongbo
收藏  |  浏览/下载:50/0  |  提交时间:2021/12/01
Genome assembly  Gap filling  Scaffolding  Optical maps  Probabilistic search  
FALCON2: a web server for high-quality prediction of protein tertiary structures 期刊论文
BMC BIOINFORMATICS, 2021, 卷号: 22, 期号: 1, 页码: 14
作者:  Kong, Lupeng;  Ju, Fusong;  Zhang, Haicang;  Sun, Shiwei;  Bu, Dongbo
收藏  |  浏览/下载:46/0  |  提交时间:2021/12/01
Protein structure prediction  Template-based modeling  Ab initio prediction  Protein structure prediction web service  
CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction 期刊论文
NATURE COMMUNICATIONS, 2021, 卷号: 12, 期号: 1, 页码: 9
作者:  Ju, Fusong;  Zhu, Jianwei;  Shao, Bin;  Kong, Lupeng;  Liu, Tie-Yan;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:42/0  |  提交时间:2021/12/01
ISSEC: inferring contacts among protein secondary structure elements using deep object detection 期刊论文
BMC BIOINFORMATICS, 2020, 卷号: 21, 期号: 1, 页码: 13
作者:  Zhang, Qi;  Zhu, Jianwei;  Ju, Fusong;  Kong, Lupeng;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:37/0  |  提交时间:2021/12/01
Protein structure  Secondary structure elements  Inter-SSE contacts  
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning (vol 20, 537, 2019) 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 期号: 1, 页码: 5
作者:  Zhang, Haicang;  Zhang, Qi;  Ju, Fusong;  Zhu, Jianwei;  Gao, Yujuan;  Xie, Ziwei;  Deng, Minghua;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:51/0  |  提交时间:2020/12/10